On 10/4/22 22:33, Nagle, Michael F wrote:
Rob Sargent
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The backslashes appear to be coming from parallel. My command has file
paths with forward slashes and these are replaced with \_ by parallel,
it seems.
To demonstrate, here is one my first command in the a I pass to parallel:
gemma -bfile ./1323_cohort_maf01_geno10.snp.pass -p
./pheno_files/callus_regeneration_PC1-uv_unique_rmoutliers_boxcox_resid.noheader.pheno
-k ./1323_cohort_maf01_geno10.cXX.txt -lmm 1 -n 3 -miss 0.1 -o
callus_regeneration_PC1-uv_unique_rmoutliers_boxcox_resid-ResidOverPhase
Here is the error for that command:
mkdir output/1/gemma -bfile .\_1323_cohort_maf01_geno10.snp.pass -p
.\_pheno_files\_callus_regeneration_PC1-uv_unique_rmoutliers_boxcox_resid.noheader.pheno
-k .\_1323_cohort_maf01_geno10.cXX.txt -lmm 1 -n 3 -miss 0.1 -o
callus_regeneration_PC1-uv_unique_rmoutliers_boxc: Invalid argument at
/home/gmobot/anaconda3/envs/gemma/bin/parallel line 12170.
Are you using backslash continuation lines by any chance?
